private IDataStoreReader GetIDataStoreReader()
{
if (_dataStoreReader == null)
_dataStoreReader = DataAccessLayer.GetIDataStoreReader();
return _dataStoreReader;
}
public void RemoveStudies(IEnumerable <string> studyInstanceUids)
{
try
{
using (IDataStoreReader reader = GetIDataStoreReader())
{
foreach (string studyUid in studyInstanceUids)
{
Study study = (Study)reader.GetStudy(studyUid);
File.Delete(study.StudyXmlUri.LocalDiskPath);
}
}
SessionManager.BeginWriteTransaction();
foreach (string uid in studyInstanceUids)
{
Session.Delete("from Study where StudyInstanceUid_ = ?", uid, NHibernateUtil.String);
}
SessionManager.Commit();
}
catch (Exception e)
{
SessionManager.Rollback();
throw new DataStoreException("Failed to clear specified studies from the data store.", e);
}
}
protected CrmGenericImporter(ILogger logger, IDataStoreReader <Entity, EntityWrapper> storeReader, DataCrmStoreWriter storeWriter, ICrmGenericImporterConfig config, CancellationToken token)
: base(logger, storeReader, storeWriter, token)
{
this.config = config;
targetEntRepo = storeWriter?.GetEntityRepository;
AddCustomProcessors();
}
IEnumerator <ISopInstance> IEnumerable <ISopInstance> .GetEnumerator()
{
using (IDataStoreReader reader = DataAccessLayer.GetIDataStoreReader())
{
foreach (string studyUID in _studyDictionary.Keys)
{
Dictionary <string, Dictionary <string, string> > studyInfo = _studyDictionary[studyUID];
Debug.Assert(studyInfo != null);
foreach (string seriesInstanceUID in studyInfo.Keys)
{
Dictionary <string, string> seriesInfo = studyInfo[seriesInstanceUID];
Debug.Assert(seriesInfo != null);
foreach (string sopInstanceUID in seriesInfo.Keys)
{
foreach (ISopInstance sopInstance in reader.GetStudy(studyUID).GetSopInstances())
{
if (sopInstance.SopInstanceUid != sopInstanceUID)
{
continue;
}
yield return(sopInstance);
break;
}
}
}
}
}
}
public TestCrmGenericImporter(
ILogger logger,
IDataStoreReader <Entity, EntityWrapper> storeReader,
DataCrmStoreWriter storeWriter,
ICrmGenericImporterConfig config)
: base(logger, storeReader, storeWriter, config)
{
}
private IDataStoreReader GetIDataStoreReader()
{
if (_dataStoreReader == null)
{
_dataStoreReader = DataAccessLayer.GetIDataStoreReader();
}
return(_dataStoreReader);
}
public AnonymizeStudyOutput AnonymizeStudy(AnonymizeStudyInput input)
{
// load study to anonymize
IDataStoreReader reader = DataAccessLayer.GetIDataStoreReader();
IStudy study = reader.GetStudy(input.StudyInstanceUID);
List <ISopInstance> sops = new List <ISopInstance>(study.GetSopInstances());
// ensure there is a valid output location
if (string.IsNullOrEmpty(input.OutputDirectory))
{
// create temp dir
}
string fullPath = Path.GetFullPath(input.OutputDirectory);
if (!Directory.Exists(fullPath))
{
Directory.CreateDirectory(fullPath);
}
// set up anonymization data
StudyData studyData = new StudyData();
studyData.PatientId = input.PatientId;
studyData.PatientsNameRaw = input.PatientsName;
studyData.PatientsBirthDate = input.PatientsBirthDate;
studyData.PatientsSex = input.PatientsSex;
studyData.AccessionNumber = input.AccessionNumber;
studyData.StudyDescription = input.StudyDescription;
studyData.StudyDate = input.StudyDate;
DicomAnonymizer anonymizer = new DicomAnonymizer();
anonymizer.StudyDataPrototype = studyData;
//The default anonymizer removes the series data, so we just clone the original.
anonymizer.AnonymizeSeriesDataDelegate =
delegate(SeriesData original) { return(original.Clone()); };
// anonymize each image in the study
for (int i = 0; i < sops.Count; ++i)
{
ISopInstance sop = sops[i];
DicomFile file = new DicomFile(sop.GetLocationUri().LocalDiskPath);
anonymizer.Anonymize(file);
file.Save(string.Format("{0}\\{1}.dcm", fullPath, i));
}
return(new AnonymizeStudyOutput(sops.Count));
}
public GenericDataMigrator(ILogger logger, IDataStoreReader <TMigrationEntity, TMigrationEntityWrapper> storeReader, IDataStoreWriter <TMigrationEntity, TMigrationEntityWrapper> storeWriter)
{
logger.ThrowIfNull <ArgumentNullException>(nameof(logger));
storeReader.ThrowIfNull <ArgumentNullException>(nameof(storeReader));
storeWriter.ThrowIfNull <ArgumentNullException>(nameof(storeWriter));
this.storeReader = storeReader;
this.storeWriter = storeWriter;
this.Logger = logger;
cancellationToken = new CancellationTokenSource().Token;
processors = new List <IEntityProcessor <TMigrationEntity, TMigrationEntityWrapper> >();
}
private void DisposeReader()
{
try
{
if (_dataStoreReader != null)
{
_dataStoreReader.Dispose();
}
}
finally
{
_dataStoreReader = null;
}
}
protected void InitializeAnnotationList(string studyInstanceUID)
{
if (_annotationDictionary.ContainsStudy(studyInstanceUID))
{
return;
}
StudyItemList studyAnnotations = GetAnnotationsList(studyInstanceUID); // TODO - switch to using SR IOD when we have it
if (studyAnnotations == null || studyAnnotations.Count == 0)
{
return;
}
using (IDataStoreReader reader = DataAccessLayer.GetIDataStoreReader())
{
foreach (StudyItem studyItem in studyAnnotations)
{
ClearCanvas.Dicom.DataStore.Study study = reader.GetStudy(studyItem.StudyInstanceUid) as ClearCanvas.Dicom.DataStore.Study;
if (study != null)
{
IEnumerable <ISeries> allSeries = study.GetSeries();
foreach (ISeries series in allSeries)
{
if (series != null && series.Modality == "SR")
{
IEnumerable <ISopInstance> sopInstances = series.GetSopInstances();
foreach (ISopInstance sopInstance in sopInstances)
{
if (sopInstance != null)
{
DicomUri fileUri = sopInstance.GetLocationUri();
if (fileUri.IsFile)
{
_annotationDictionary.Add(study.StudyInstanceUid, series.SeriesInstanceUid, sopInstance.SopInstanceUid, fileUri.LocalDiskPath);
}
}
}
}
}
}
}
// TODO:
// 1. Find and load all annotations (read-only?)
// LocalDataStoreActivityMonitor.Instance.
}
}
public void ClearAllStudies()
{
try
{
using (IDataStoreReader reader = GetIDataStoreReader())
{
foreach (Study study in reader.GetStudies())
{
File.Delete(study.StudyXmlUri.LocalDiskPath);
}
}
SessionManager.BeginWriteTransaction();
Session.Delete("from Study");
SessionManager.Commit();
}
catch (Exception e)
{
SessionManager.Rollback();
throw new DataStoreException("Failed to clear all studies from the data store.", e);
}
}
public GenericDataMigrator(ILogger logger, IDataStoreReader <TMigrationEntity, TMigrationEntityWrapper> storeReader, IDataStoreWriter <TMigrationEntity, TMigrationEntityWrapper> storeWriter, CancellationToken cancellationToken)
: this(logger, storeReader, storeWriter)
{
this.cancellationToken = cancellationToken;
}
/// <summary>
/// Deserializes the specified xml log file.
/// </summary>
/// <param name="reader">The <see cref="IDataStoreReader"/> to use.</param>
/// <returns>The deserialized log entries.</returns>
public static List<LogEntry> Deserialize( IDataStoreReader reader )
{
var list = new List<LogEntry>();
reader.Read(
"LogEntries",
() =>
{
while( reader.Read()
&& reader.Token == DataStoreToken.ObjectStart )
list.Add(reader.Deserialize(LogEntry.Serializer.Default));
});
return list;
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="reader"></param>
public DataStoreInfo(IDataStoreReader reader)
{
this.Name = reader.GetName();
this.Description = reader.GetDescription();
this.IsFdoEnabled = reader.GetIsFdoEnabled();
}
private void DisposeReader()
{
try
{
if (_dataStoreReader != null)
_dataStoreReader.Dispose();
}
finally
{
_dataStoreReader = null;
}
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="reader"></param>
public DataStoreInfo(IDataStoreReader reader)
{
this.Name = reader.GetName();
this.Description = reader.GetDescription();
this.IsFdoEnabled = reader.GetIsFdoEnabled();
}
public GenericCrmDataMigrator(ILogger logger, IDataStoreReader <Entity, EntityWrapper> storeReader, IDataStoreWriter <Entity, EntityWrapper> storeWriter)
: base(logger, storeReader, storeWriter)
{
}
public GenericCrmDataMigrator(ILogger logger, IDataStoreReader <Entity, EntityWrapper> storeReader, IDataStoreWriter <Entity, EntityWrapper> storeWriter, CancellationToken cancellationToken)
: base(logger, storeReader, storeWriter, cancellationToken)
{
}